When does an enquiry start?

Following the completion of a client's 2010 Tax Return information came to light which suggested that income had been omitted from the 2009 Tax Return. We submitted an amended 2009 Tax Return electronically and received the electronic acknowledgement of receipt from both my software (IRIS) and HMRC.

Two days later we received a S9A notice. The date on the notice was five days earlier i.e. three days before we submitted the amended Return.

HMRC state that the enquiry stands because it was opened prior to the filing of the amended Return and they also state that the Return was not accepted because the file had been marked as being under enquiry - they told me that I should have received a rejection notice.

Incidentally they raised their enquiry on the very issue that we amended the Return for but where do we stand with potential penalties etc?